Understanding and acting on biodiversity loss requires robust tools linking biodiversity impacts to land use change, the biggest threat to terrestrial biodiversity. Here we estimate agriculture's impact on the Brazilian Cerrado's biodiversity using three approaches-countryside Species-Area Relationship, Species Threat Abatement and Restoration and Species Habitat Index. By using same input data, we show how indicator scope and design affects impact assessments and resulting decision-support. All indicators show agriculture expansion's increasing pressure on biodiversity. Results suggest that metrics are complementary, providing distinctly different insight into biodiversity change drivers and impacts. Meaningful applications of biodiversity indicators therefore require compatibility between focal questions and indicator choice regarding temporal, spatial, and ecological perspectives on impact and drivers. Backward-looking analyses focused on historical land use change and accountability are best served by the countryside-Species Area Relationship and the Species Habitat Index. Forward-looking analyses of impact risk hotspots and global extinctions mitigation are best served by the Species Threat Abatement and Restoration.